CompareValues.SJ.DonorLevel.10x: Differential splice junction analysis at donor level

In wenweixiong/MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Differential splice junction analysis at donor level

Description

Performs differential splice junction analysis between two groups of cells by aggregating cells by their corresponding donor IDs. Statistical test used here is the permutation test.

Usage

CompareValues.SJ.DonorLevel.10x(
  MarvelObject,
  cell.group.list,
  min.pct.cells.gene.expr = 10,
  min.n.cells.gene.expr = 10,
  min.gene.counts.total = 3,
  min.sj.count = 1,
  min.donor.gene.expr = 3,
  min.donor.sj.expr = 3
)

Arguments

MarvelObject	cell.group.list List of character strings. List defining the two cell groups and their respective donor IDs and their corresponding cells IDs.
min.pct.cells.gene.expr	Numeric value. Mininum percentage of cells across a donor expressing a given gene for that gene to be considered expressed. Genes below this threshold will be considered not expressed. Default is 10. To be used in conjunction with min.n.cells.gene.expr and min.gene.counts.total.
min.n.cells.gene.expr	Numeric value. Mininum number of cells across a donor expressing a given gene for that gene to be considered expressed. Genes below this threshold will be considered not expressed. Default is 10. To be used in conjunction with min.pct.cells.gene.expr and min.gene.counts.total.
min.gene.counts.total	Numeric value. Mininum number of UMI counts across a donor for that gene to be considered expressed. Genes below this threshold will be considered not expressed. Default is 3. To be used in conjunction with min.n.cells.gene.expr and min.pct.cells.gene.expr.
min.sj.count	Numeric value. Mininum number of UMI counts across a donor for that splice junction to be considered expressed. Splice junctions below this threshold will be considered not expressed. Default is 1.
min.donor.gene.expr	Numeric value. Minimum number of donors expressing a given gene based on min.pct.cells.gene.expr, min.n.cells.gene.expr, and min.gene.counts.total options for that gene to be included for analysis. Default is 3.
min.donor.sj.expr	Numeric value. Minimum number of donors expressing a given splice junction based on min.sj.count option for that splice junction to be included for analysis. Default is 3.

Value

An object of class S3 with a new slots MarvelObject$DE$Pseudobulk$SJ$Table and MarvelObject$DE$Pseudobulk$SJ$cell.group.list.

wenweixiong/MARVEL documentation built on Aug. 5, 2024, 2:54 p.m.